Pucker up, Buttercup, and head to the kitchen to make these lemon protein muffins. They have all the bright, citrusy flavor you crave, and they’re easy to make too. A perfect treat to wake up your senses on a dreary morning!
Thanks to a blend of cottage cheese and protein powder, they deliver a soft, moist crumb that practically melts in your mouth. They are a delightful addition to any high protein, low carb breakfast. And diehard lemon lovers might even want to spread them with a little keto lemon curd!

Sometimes I need a reminder about how much I love lemon. I tend to reach for chocolate treats over and above anything else. But whenever I taste it, I am always amazed by how that tangy bright flavor dances on my tongue.
It’s what makes recipes like keto lemon cheesecake bars and keto lemon sugar cookies so popular. And I know my fellow lemon lovers will be delighted with this new muffin recipe. The fact that it adds 12 grams of protein doesn’t hurt either!

Why You Will Love This Recipe
- Bright citrus flavor: Fresh lemon juice and zest give these muffins that classic lemon poppyseed taste.
- High-protein: Made with cottage cheese and protein powder, they are a great way to add a little more protein into your day.
- Keto and gluten-free: No grains, gluten, or sugar!
- Moist and tender: Cottage cheese helps create an incredibly soft, tender texture that is out of this world.
- Great for meal prep: They store and freeze beautifully. Perfect for quick high protein snacks.
Ingredient Notes

- Cottage cheese: Any percentage of milk fat should work well in these muffins. If you prefer, you can use ricotta but it’s a little lower in protein.
- Almond flour: Fine blanched almond flour will give you the best texture for all your keto baked goods.
- Sweetener: I recommend an erythritol based sweetener so the muffins don’t get too dark. Allulose can work but it may brown the muffins a lot faster, particularly on the bottoms.
- Protein powder: Whey protein powder or egg white protein powder work best. Plant based will work but may change the color of your muffins. Do not use collagen as it will make them very gummy and hard to cook through.
- Lemon: You will need the zest and juice from a lemon.
- Poppy seeds: The addition of poppy seeds adds delicious crunch and a unique flavor.
- Baking staples: Eggs, baking powder, and salt.
How to Make Lemon Poppyseed Protein Muffins

- Blend the wet ingredients: Place the cottage cheese, eggs, and sweetener in a blender and blend until smooth.
- Blend the dry ingredients: Add the almond flour, protein powder, baking powder, and salt, and blend again.
- Add the lemon: Zest the lemon and add to the blender, then squeeze in fresh lemon juice.
- Add the poppy seeds: Stir them into the batter by hand, so they don’t get blended up.
- Bake the muffins. Divide the batter between the muffin cups and bake until the tops are puffed and just firm to the touch.
- Enjoy!

Tips for Success
Blend the batter: Don’t skip this, as it makes the batter silky smooth and avoids little clumps of cheese in the muffins.
Don’t over-bake: Protein powder has a way of drying out baked goods if you cook them too long. Make sure to take them out the minute the tops are puffed and set to the touch, with no sponginess underneath.
Let them cool, but not too long! I found that once the muffins were fully cool, they started sticking to the silicone liners. My recommendation is to cool them 15 to 20 minutes, then gently remove them from the muffin liners.
Boost the lemon if you love tang: A little lemon extract or extra zest takes them into bakery-style territory.

Lemon Poppyseed Protein Muffins
Ingredients
- 1 cup cottage cheese
- 3 large eggs
- 1/2 cup granular sweetener
- 1 3/4 cup almond flour
- 1/2 cup whey protein powder, (vanilla or unflavored)
- 2 tsp baking powder
- 1/4 tsp salt
- Zest of one lemon
- 3 tbsp fresh lemon juice
- 1 1/2 tbsp poppyseeds
Instructions
- Preheat the oven to 325ºF and line a standard muffin pan with 12 silicone or parchment liners.
- Place the cottage cheese, eggs, and sweetener in a blender and blend until smooth.
- Add the almond flour, protein powder, baking powder, and salt, and blend again. Then add the lemon zest and lemon juice and blend until everything is incorporated.
- If the batter is overly thick, add more liquid 1 tablespoon at a time until it is a thick but pourable batter. Stir in the poppyseeds.
- Divide the batter between the muffin cups, filling almost all the way to the top. Bake 25 to 30 minutes, until the tops are puffed and just firm to the touch.
- Remove and let cool in the pan. But make sure to get them out of the silicone liners soon after they are cool to the touch (they tend to start sticking again as they cool off).
Notes
Nutrition
Frequently Asked Questions
No. Once blended and baked into the muffin, the flavor disappears. All you’ll notice is a moist, tender muffin with a bright, fresh flavor.
This recipe relies on the protein and moisture from cottage cheese or ricotta. I don’t know that there is a good replacement for that without ruining the consistency.
These lemon poppyseed protein muffins have 5.2g of carbs and 2.0g of fiber per serving. That comes to 3.2g net carbs per muffin.
Nutritional Disclaimer
Please note that I am not a medical or nutritional professional. I am simply recounting and sharing my own experiences on this blog. Nothing I express here should be taken as medical advice and you should consult with your doctor before starting any diet or exercise program. I provide nutritional information for my recipes simply as a courtesy to my readers. It is calculated using MacGourmet software and I remove erythritol from the final carb count and net carb count, as it does not affect my own blood glucose levels. I do my best to be as accurate as possible but you should independently calculate nutritional information on your own before relying on them. I expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website.
Free Bonus: Secrets to Keto Baking!
Sign up for your favorite recipes delivered straight to your inbox plus get our FREE bonus: Secrets to Keto Baking!






I made these exactly as written but I did not find them sweet enough. I made a glaze of powdered erythritol and milk and that helped.
I used the bottled Key Lime Juice, a splash of lime flavoring, and placed a few SF white chocolate chips on top. They turned out amazing! Will 100% make again. Carolyn, thank you for all you do!
How lovely!